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Microbial Ecology
Lecture 1
The term “microbial ecology” is now used in a general way to
describe the presence and contributions of microorganisms, through
their activities, to the places where they are found. Much of the
information on microbial presence and contributions to soils, waters,
and associations with plants, now described by this term, would have
been considered as “environmental microbiology” in the past. Thomas
D. Brock, the discoverer of Thermus aquaticus, has given a definition of
microbial ecology that may be useful: “Microbial ecology is the study of
the behavior and activities of microorganisms in their natural
environments.” The important operator in this sentence is their
environment instead of the environment. To emphasize this point, Brock
has noted that “microbes are small; their environments also are small.”
In these small environments or “microenvironments,” other kinds of
microorganisms (and macroorganisms) often also are present.
Environmental microbiology, in comparison, relates primarily to
all-over microbial processes that occur in a soil, water, or food, as
examples. It is not concerned with the particular “microenvironment”
where the microorganisms actually are functioning, but with the
broader-scale effects of microbial presence and activities. One can study
these microbially mediated processes and their possible global impacts
at the scale of “environmental microbiology” without knowing about the
specific microenvironment (and the organisms functioning there) where
these processes actually take place. However, it is critical to be aware
that microbes function in their localized environments and affect
ecosystems at greater scales, including causing global-level effects. In
the last decades the term “microbial ecology” largely has lost its original
meaning, and recently the statement has been made that “microbial
ecology has become a ‘catch-all’ term.”
Foundations of Microbial Ecology
Two major themes will be studied, the nature of microbial
relationships with other living organisms, or the nature of symbioses,
and the interactions of these organisms with each other and with their
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nonliving physical environment, or the area of microbial ecology. The
term symbiosis is used in its original broadest sense, as an association of
two or more different species of organisms.
Microorganisms function as populations or assemblages of similar
organisms, and as communities, or mixtures of different microbial
populations. These microorganisms have evolved while interacting with
the inorganic world and with higher organisms, and they largely play
beneficial and vital roles; disease-causing organisms are only a minor
component of the microbial world. Microorganisms, as they interact
with other organisms and their environment, also contribute to the
functioning of ecosystems, or self-regulating biological communities and
their physical environment. Knowledge of these interactions is
important in understanding both microbial contributions to the natural
world and microbial roles in disease processes.
A major problem in understanding microbial interactions is that
most microscopically observable microorganisms cannot be grown in
laboratory. The differences between observable and culturable
microorganisms, which limit this field even today, have been noted for
at least 70 years. This problem was discussed by Selman Waksman, the
discoverer of streptomycin, and has not yet been solved. The use of
molecular techniques, however, is providing valuable information on
these still uncultured microorganisms, and rapid progress is being made
in this area. This remains as a central challenge in attempting to
understand microbial interactions, microbial ecology, and biology itself.
Microbial Interactions
Microorganisms can be physically associated with other organisms
in a variety of ways. One organism can be located on the surface of
another, as an ectosymbiont, in this case, the ectosymbiont usually is a
smaller organism located on the surface of a larger organism. Often,
dissimilar organisms of similar size are in physical contact. The term
consortium can be used to describe this physical relationship. Consortia
in aquatic environments are complex, involving multiple layers of
similar-looking microorganisms that often have complementary
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physiological properties. In contrast, one organism can be located within
another organism as an endosymbiont. There also are many cases in
which microorganisms live on both the inside and the outside of another
organism, a phenomenon called ecto/endosymbiosis. Interesting
examples of ecto/endosymbiosis include a Thiothrix species, a sulfurusing bacterium, which is attached to the surface of a mayfly larva and
which itself contains a parasitic bacterium. Mycorrhizal fungi often
contain endosymbiotic bacteria, as well as having bacteria living on their
surfaces. These physical associations can be intermittent and cyclic or
permanent. The following table showing the intermittent and cyclic
associations of microorganisms with plants and marine animals
Intermittent and Cyclical Symbioses of Microorganisms with Plants and Marine
Cyclical Symbiont
Gunnera (tropical angiosperm)
Nostoc (cyanobacterium)
Azolla (rice paddy fern)
Phaseollus (bean)
Rhizobium (N2 fixer)
Ardisia (angiosperm)
Coral coelenterates
Luminous fish
Vibrio, Photobacterium
Photobacterium fischerei
Important human diseases, including listeriosis, malaria,
leptospirosis, legionellosis, and vaginosis also involve such intermittent
and cyclic symbioses. Interesting permanent relationships also occur
between bacteria and animals, as shown in the table below.
Examples of Permanent Bacterial-Animal Symbioses and the Characteristics
Contributed by the Bacterium to the Symbiosis
Animal Host
Sepiolid squid (Euprymna
Medicinal leech (Hirudo
Aphid (Schizaphis
Nematode worm
(Heterorhabditis spp.)
Shipworm mollusk
Symbiont Contribution
Luminous bacterium
Luminescence (Vibrio fisheri)
Enteric bacterium (Aeromonas
Bacterium (Buchnera
Luminous bacterium
(Photorhabdus luminescens)
Gill cell bacterium
Blood digestion
Amino acid synthesis
Predation and antibiotic
Cellulose digestion and
nitrogen fixation
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Hosts include squid, leeches, aphids, nematodes, and mollusks. In
each of these cases, an important characteristic of the host animal is
conferred by the permanent bacterial symbiont. Although it is possible
to observe microorganisms in these varied physical associations with
other organisms, the fact that there is some type of physical contact
provides no information on the types of interactions that might be
occurring. These interactions can be positive (mutualism,
protocooperation, and commensalism) or negative (predation,
parasitism, amensalism, and competition) as shown in figure below.
Mutualism (Latin mutuus, borrowed or reciprocal) defines the
relationship in which some reciprocal benefit accrues to both partners.
This is an obligatory relationship in which the mutualist and the host are
metabolically dependent on each other. Several examples of mutualism
are presented next. The protozoan-termite relationship is a classic
example of mutualism in which the flagellated protozoa live in the gut of
termites and wood roaches (The right picture (a)).
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Light micrographs of (a) a worker termite of the genus Reticulitermes eating wood (×10), and (b)
Trichonympha, a multiflagellated protozoan from the termite’s gut (×135). Notice the many flagella
that occur over most of its length. The ability of Trichonympha to break down cellulose enables
termites to use wood as a food source.
These flagellates exist on a diet of carbohydrates, acquired as
cellulose ingested by their host (the left picture (b)). The protozoa engulf
wood particles, digest the cellulose, and metabolize it to acetate and
other products. Termites oxidize the acetate released by their
flagellates. Because the host is almost always incapable of synthesizing
cellulases, it is dependent on the mutualistic protozoa for its existence.
This mutualistic relationship can be readily tested in the
laboratory if wood roaches are placed in a bell jar containing woodchips
and a high concentration of O2. Because O2 is toxic to the flagellates,
they die. The wood roaches are unaffected by the high O2 concentration
and continue to ingest wood, but they soon die of starvation due to a
lack of cellulases. Lichens are another excellent example of mutualism
(the figure below). Lichens are the association between specific
ascomycetes (the fungus) and certain genera of either green algae or
cyanobacteria. In lichen, the fungal partner is termed the mycobiont and
the algal or cyanobacterial partner, the phycobiont.
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Crustose (encrusting) lichens growing on a granite post.
Because the phycobiont is a photoautotroph—dependent only on
light, carbon dioxide, and certain mineral nutrients—the fungus can get
its organic carbon directly from the alga or cyanobacterium. The fungus
often obtains nutrients from its partner by haustoria (projections of
fungal hyphae) that penetrate the phycobiont cell wall. It also uses the
O2 produced during phycobiont photophosphorylation in carrying out
respiration. In turn, the fungus protects the phycobiont from excess light
intensities, provides water and minerals to it, and creates a firm
substratum within which the phycobiont can grow protected from
environmental stress.
Sulfide-Based Mutualisms:
Tube worm–bacterial relationships exist several thousand meters
below the surface of the ocean, where the Earth’s crustal plates are
spreading apart (the figure below). Vent fluids are anoxic, contain high
concentrations of hydrogen sulfide, and can reach a temperature of
350°C. The seawater surrounding these vents has sulfide concentrations
around 250 µM and temperatures 10 to 20°C above the normal
seawater temperature of 2.1°C. The giant (>1 m in length), red, gutless
tube worms (Riftia spp.) near these hydrothermal vents provide an
example of a unique form of mutualism and animal nutrition in which
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chemolithotrophic bacterial endosymbionts are maintained within
specialized cells of the tube worm host (the last figure below).
Basic Structure of a Hydrothermal Vent with its Mutualistic Microbe-Animal Associations
Reduced chemicals including sulfide are released as seawater penetrates the fractured basaltic ocean
floor, is heated, and returns as vent fluid to the ocean, creating environments for growth of the tube
worms and their prokaryotic mutualists.
To date, all attempts to culture these microorganisms have been
unsuccessful. The tube worm takes up hydrogen sulfide from the sea
water and binds it to hemoglobin (the reason the worms are bright red).
The hydrogen sulfide is then transported in this form to the bacteria,
which use the sulfide-reducing power to fix carbon dioxide in the Calvin
cycle. The CO2 required for this cycle is transported to the bacteria in
three ways:
1- Freely dissolved in the blood.
2- Bound to hemoglobin.
3- In the form of organic acids such as malate and succinate.
These acids are decarboxylated to release CO2 in the trophosome, the
tissue containing bacterial symbionts. Using these mechanisms, the
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bacteria synthesize reduced organic material from inorganic substances.
The organic material is then supplied to the tube worm through its
circulatory system and serves as the main nutritional source for the
tissue cells.
The Tube Worm—Bacterial Relationship.
(a) A community of tube worms (Riftia pachyptila) at the Galapagos Rift hydrothermal vent site (depth
2,550 m). Each worm is more than a meter in length and has a 20 cm gill plume. (b, c) Schematic
illustration of the anatomical and physiological organization of the tube worm. The animal is anchored
inside its protective tube by the vestimentum. At its anterior end is a respiratory gill plume. Inside the
trunk of the worm is a trophosome consisting primarily of endosymbiotic bacteria, associated cells,
and blood vessels. At the posterior end of the animal is the opisthosome, which anchors the worm in
its tube. (d) Oxygen, carbon dioxide, and hydrogen sulfide are absorbed through the gill plume and
transported to the blood cells of the trophosome. Hydrogen sulfide is bound to the worm’s
hemoglobin (HSHbO2) and carried to the endosymbiont bacteria. The bacteria oxidize the hydrogen
sulfide and use some of the released energy to fix CO2 in the Calvin cycle. Some fraction of the
reduced carbon compounds synthesized by the endosymbiont is translocated to the animal’s tissues.